🧙Player 1
Ondrej Mottl
Assistant Professor at Charles University
Head of the 🧑💻 Laboratory of Quantitative Ecology
🔓The Shortcut
VegVault + {vaultkeepr}
🔓The Shortcut
VegVault + {vaultkeepr}
With few lines of code, you can:
🔓The Shortcut
VegVault + {vaultkeepr}
With few lines of code, you can:
- Connect to the VegVault database
- Access vegetation, trait, and climate data simultaneously
🔓The Shortcut
VegVault + {vaultkeepr}
With few lines of code, you can:
- Connect to the VegVault database
- Access vegetation, trait, and climate data simultaneously
- Filter by spatial-temporal boundaries
data_rockies <-
vaultkeepr::open_vault(
path = "<path_to_VegVault>"
) %>%
vaultkeepr::get_datasets() %>%
vaultkeepr::select_dataset_by_geo(
lat_lim = c(30, 50),
long_lim = c(-120, -100)
) %>%
vaultkeepr::get_samples() %>%
vaultkeepr::select_samples_by_age(
age_lim = c(0, 20000) # 20,000 BP
) %>%
vaultkeepr::get_taxa() %>%
vaultkeepr::get_abiotic_data() %>%
vaultkeepr::get_traits()🔓The Shortcut
VegVault + {vaultkeepr}
With few lines of code, you can:
- Connect to the VegVault database
- Access vegetation, trait, and climate data simultaneously
- Filter by spatial-temporal boundaries
- Harmonise taxonomy
data_rockies <-
vaultkeepr::open_vault(
path = "<path_to_VegVault>"
) %>%
vaultkeepr::get_datasets() %>%
vaultkeepr::select_dataset_by_geo(
lat_lim = c(30, 50),
long_lim = c(-120, -100)
) %>%
vaultkeepr::get_samples() %>%
vaultkeepr::select_samples_by_age(
age_lim = c(0, 20000) # 20,000 BP
) %>%
vaultkeepr::get_taxa(
classify_to = "genus"
) %>%
vaultkeepr::get_abiotic_data() %>%
vaultkeepr::get_traits(
classify_to = "genus"
)🔓The Shortcut
VegVault + {vaultkeepr}
With few lines of code, you can:
- Connect to the VegVault database
- Access vegetation, trait, and climate data simultaneously
- Filter by spatial-temporal boundaries
- Harmonise taxonomy
- Get data in tidy format
data_rockies <-
vaultkeepr::open_vault(
path = "<path_to_VegVault>"
) %>%
vaultkeepr::get_datasets() %>%
vaultkeepr::select_dataset_by_geo(
lat_lim = c(30, 50),
long_lim = c(-120, -100)
) %>%
vaultkeepr::get_samples() %>%
vaultkeepr::select_samples_by_age(
age_lim = c(0, 20000) # 20,000 BP
) %>%
vaultkeepr::get_taxa(
classify_to = "genus"
) %>%
vaultkeepr::get_abiotic_data() %>%
vaultkeepr::get_traits(
classify_to = "genus"
) %>%
vaultkeepr::extract_data()🔓The Shortcut
VegVault + {vaultkeepr}
With few lines of code, you can get the data you need to answer:
Did vegetation in the Rocky Mountains remain functionally stable under climate change from the LGM to the present?
data_rockies <-
vaultkeepr::open_vault(
path = "<path_to_VegVault>"
) %>%
vaultkeepr::get_datasets() %>%
vaultkeepr::select_dataset_by_geo(
lat_lim = c(30, 50),
long_lim = c(-120, -100)
) %>%
vaultkeepr::get_samples() %>%
vaultkeepr::select_samples_by_age(
age_lim = c(0, 20000) # 20,000 BP
) %>%
vaultkeepr::get_taxa(
classify_to = "genus"
) %>%
vaultkeepr::get_abiotic_data() %>%
vaultkeepr::get_traits(
classify_to = "genus"
) %>%
vaultkeepr::extract_data()🔓The Shortcut
🆙LevelUp
- A global SQLite database linking interdisciplinary plot-based vegetation data!
- Links to functional traits, climate variables, and soil properties
- Built for exploring biodiversity dynamics across time & space
- Open Source & Reproducible
🗃️The Source Code
~110 GB | 32 tables & 87 variables | 480,000+ Datasets | 13M+ Samples | 110,000+ Taxa | 11M+ Trait values | 8 Abiotic variables
Data sources
- 🌿 Paleoecological records (Neotoma, FOSSILPOL)
- 🌱 Contemporary vegetation (sPlotOpen, BIEN)
- 🌾 Functional traits (BIEN, TRY)
- 🌍 Climate & soil data (CHELSA, WoSIS)
💎Key Innovations
- Abiotic context
- Sample-specific climate and soil data
- paleo and contemporary
- mapped to spatio-temporal grids
- Selected variables for vegetation studies
- e.g. temperature, precipitation, soil type, etc.
🛠️Controls
An Open Source R package📦 - Your key🔑 to VegVault
- ✅ No SQL required - just load & go!
- ✅ Filter by taxa, traits, time & space
- ✅ Tidyverse-compatible interface
- ✅ Directly usable in R for analysis
- 🔗 Learn more: bit.ly/vaultkeepr
💾 Save & Share
Everything! is publically available and reproducible!
- VegVault
- Fully reproducible workflows via GitHub and Zenodo (Modular, version-controlled pipelines with metadata)
- vaultkeepr
- Open Source tested R package with documentation
- Join the quest!
💡Side Quests
The world is your oyster!
- Reconstruct long-term diversity patterns
- Investigate trait-based community assembly
- Explore biome transitions and shifts
- Quantify ecological novelty and functional turnover
- Test trait-environment relationships across time
📜Credits
VegVault database: linking global paleo-, and neo-vegetation data with functional traits and abiotic drivers
👤P1: Ondřej Mottl
📅2025-08-02
📍IAVS, Colorado, USA
